Molecular biology, darwinism and nomogenesis

The theory of nomogenesis put forward by L. S. Berg in 1922 is discussed. It is shown that side by side with some erroneous anti-darwinian ideas the theory contains a series of important suggestions which anticipate the further development of the synthetic theory of evolution. Berg has foreseen the development of molecular biology. Thus he was the fore-teller of our branch of science. The theory of nomogenesis emphasized the limitations of natural selection which determine the directionality of evolution. Berg treated the speciation as a kind of phase transition. Even the most conscientious critics of Berg have misrepresented the real sense of his works. It is totally groundless to treat nomogenesis as an idealistic of Lamarkian theory. Berg was superior to his critics. However the enthusiasm about nomogenesis in our time shows the inability to separate "the grains from weeds".     

Speciation and bifurcations

The interrelations of physics and biology are discussed. It is shown that Darwin can be considered as one of the founders of the important field of contemporary physics called physics of dissipative structures or synergetics. The theories of gradual and punctual evolution are presented. The contradiction between these theories can be solved on the basis of molecular theory of evolution and on the basis of the phenomenological physical treatment. The general physical properties of living systems, considered as open systems being far from equilibrium, are listed and simple non-linear mathematical models describing gradual and punctual speciation are suggested. The usual pictures which present these two kinds of speciation can possess physico-mathematical sense. Punctuated speciation means bifurcation, a kind of non-equilibrium phase transition.     

Biopolymers and evolution

Biopolymers are usually studied being extracted from the whole system of a cell or of an organism. Some important features are lost during such a procedure. It is necessary to take into account the behavior of proteins and nucleic acids in metabolic networks and to investigate their evolution. The substitutions of amino-acids metabolic networks residues are biologically possible in the polypeptides and proteins if they do not influence their spatial structure and function. The correlations of the primary structure with these properties are degenerate. The protein can be treated as "an edited statistical copolymer" (Ptitsyn). In the process of "edition" an important role is played by the ions of transient metals. Nucleic acids possess similar properties. It can be shown that the deleterious mutations of proteins can be compensated by the changes of their amount, spatial and temporal characteristics of the synthesis. Not only the structure of the protein is important but also the exact answers of the questions: how much, when and where? The contemporary theory of evolution unites phylogeny and onthogeny. The directionality of evolution is determined both by natural selection and by the already existing structure of an organism. Hence many characters are not adaptive. This is valid also for the molecular level of the structure. Thus three independent groups of facts and suggestions are presented, which confirm the neutral theory of evolution (Kimura) and elucidate its physical meaning. The molecular evolution does not coincide with the biological evolution.     

A complex speciation-richness relationship in a simple neutral model

Speciation is the "elephant in the room" of community ecology. As the ultimate source of biodiversity, its integration in ecology's theoretical corpus is necessary to understand community assembly. Yet, speciation is often completely ignored or stripped of its spatial dimension. Recent approaches based on network theory have allowed ecologists to effectively model complex landscapes. In this study, we use this framework to model allopatric and parapatric speciation in networks of communities. We focus on the relationship between speciation, richness, and the spatial structure of communities. We find a strong opposition between speciation and local richness, with speciation being more common in isolated communities and local richness being higher in more connected communities. Unlike previous models, we also find a transition to a positive relationship between speciation and local richness when dispersal is low and the number of communities is small. We use several measures of centrality to characterize the effect of network structure on diversity. The degree, the simplest measure of centrality, is the best predictor of local richness and speciation, although it loses some of its predictive power as connectivity grows. Our framework shows how a simple neutral model can be combined with network theory to reveal complex relationships between speciation, richness, and the spatial organization of populations.     

Mikroevolution — Makroevolution — Punktualismus Ein Diskussionsbeitrag am Beispiel miozäner Eomyiden (Mammalia,Rodentia)

Based on new material of the rodent genus Pseudotheridomys from the lower Miocene fissurefilling of Schaffhausen near Harburg (Nördlinger Ries, Bavaria) the process of continuous development from Pseudotheridomys to Ligerimys can be demonstrated. Within homogeneous populations of Pseudotheridomys the origin of a new morphotype can be observed. In following populations from several biostrati-graphic levels in southern Germany this type becomes more and more dominant, up to homogeneous populations of Ligerimys florancei. For this example of microevolutionary origin of a new genus — for a long time separated from its forerunner by a large gap in documentation — it is shown that neither a dichotomy nor any special mechanism of macroevolution nor a speciation in the sense of punctualism is necessary to explain its development. The process continued for at least 3 million years. It quite corresponds to the synthetic theory of evolution.     

Bindin from a sea star

SUMMARY The genetic basis for the evolution of development includes genes that encode proteins expressed on the surfaces of sperm and eggs. Previous studies of the sperm acrosomal protein bindin have helped to characterize the adaptive evolution of gamete compatibility and speciation in sea urchins. The absence of evidence for bindin expression in taxa other than the Echinoidea has limited such studies to sea urchins, and led to the suggestion that bindin might be a sea urchin-specific molecule. Here we characterize the gene that encodes bindin in a broadcast-spawning asterinid sea star ( Patiria miniata ). We describe the sequence and domain structure of a full-length bindin cDNA and its single intron. In comparison with sea urchins, P. miniata bindin is larger but the two molecules share several general features of their domain structure and some sequence features of two domains. Our results extend the known evolutionary history of bindin from the Mesozoic (among the crown group sea urchins) into the early Paleozoic (and the common ancestor of eleutherozoans), and present new opportunities for understanding the role of bindin molecular evolution in sexual selection, life history evolution, and speciation among sea stars.     

Willis, K.J., McElwain, J.C. The evolution of plants

This book, aimed at undergraduates, deals mostly with the informationthat can be gleaned about plant evolution from the fossil record.In some sense, its broad title is slightly misleading becauseother topics central to plant evolution such as genetic changein populations and mechanisms of speciation are hardly covered.After a brief introduction to the geological timescale, typesof fossil and how they are dated, the central six chapters formingthe bulk of the book follow a chronological journey. This takesthe reader from the appearance of the first photosynthesizers,to the colonization of the land, through to the evolution anddominance of     

Costameres, focal adhesions, and cardiomyocyte mechanotransduction

Mechanotransduction refers to the cellular mechanisms by which load-bearing cells sense physical forces, transduce the forces into biochemical signals, and generate appropriate responses leading to alterations in cellular structure and function. This process affects the beat-to-beat regulation of cardiac performance but also affects the proliferation, differentiation, growth, and survival of the cellular components that comprise the human myocardium. This review focuses on the experimental evidence indicating that the costamere and its structurally related structure the focal adhesion complex are critical cytoskeletal elements involved in cardiomyocyte mechanotransduction. Biochemical signals originating from the extracellular matrix-integrin-costameric protein complex share many common features with those signals generated by growth factor receptors. The roles of key regulatory kinases and other muscle-specific proteins involved in mechanotransduction and growth factor signaling are discussed, and issues requiring further study in this field are outlined.     

Drosophila melanogaster and D. simulans rescue strains produce fit offspring,despite divergent centromere-specific histone alleles

The interaction between rapidly evolving centromere sequences and conserved kinetochore machinery appears to be mediated by centromere-binding proteins. A recent theory proposes that the independent evolution of centromere-binding proteins in isolated populations may be a universal cause of speciation among eukaryotes. In Drosophila the centromere-specific histone, Cid (centromere identifier), shows extensive sequence divergence between D. melanogaster and the D. simulans clade, indicating that centromere machinery incompatibilities may indeed be involved in reproductive isolation and speciation. However, it is presently unclear whether the adaptive evolution of Cid was a cause of the divergence between these species, or merely a product of postspeciation adaptation in the separate lineages. Furthermore, the extent to which divergent centromere identifier proteins provide a barrier to reproduction remains unknown. Interestingly, a small number of rescue lines from both D. melanogaster and D. simulans can restore hybrid fitness. Through comparisons of cid sequence between nonrescue and rescue strains, we show that cid is not involved in restoring hybrid viability or female fertility. Further, we demonstrate that divergent cid alleles are not sufficient to cause inviability or female sterility in hybrid crosses. Our data do not dispute the rapid divergence of cid or the coevolution of centromeric components in Drosophila; however, they do suggest that cid underwent adaptive evolution after D. melanogaster and D. simulans diverged and, consequently, is not a speciation gene.     

Symbiotic sympatric speciation: consequence of interaction-driven phenotype differentiation through developmental plasticity

 A mechanism of sympatric speciation is presented based on the interaction-induced developmental plasticity of phenotypes. First, phenotypes of individuals with identical genotypes split into a few groups, according to instability in the developmental dynamics that are triggered with the competitive interaction among individuals. Then, through mutational changes in the genes, the phenotypic differences are fixed to genes, until the groups are completely separated in genotype as well as phenotype. It is also demonstrated that the proposed theory leads to hybrid sterility under sexual recombination, and thus speciation is completed in the sense of reproductive isolation. As a result of this postmating isolation, the mating preference evolves later. When there are two alleles, the correlation between alleles is formed to consolidate speciation. When individuals are located apart in space, different species are later segregated spatially, implying that the speciation so far regarded to be allopatric may be a result of sympatric speciation. Relationships to previous theories, frequency-dependent selection, reinforcement, Baldwin's effect, phenotypic plasticity, and resource competition are briefly discussed. Relevance of the results to natural evolution is discussed, including punctuated equilibrium, incomplete penetrance in mutants, and the change in flexibility in genotype–phenotype correspondence. Finally, we discuss how our theory is confirmed both in the field and in the laboratory, in an experiment using Escherichia coli. Received: January 30, 2002 / Accepted: May 13, 2002     

Noninteracting local-structure model of folding and unfolding transition in globular proteins. I. Formulation

A statistical-mechanical model (a noninteracting local structure model) of folding and unfolding transition in globular proteins is described and a formulation is given to calculate the partition function. The process of transition is discussed in this model within the framework of equilibrium statistical mechanics. In order to clarify the range of applicability of such an approach, the characteristics of the folding and unfolding transition in globular proteins are analyzed from the statistical-physical point of view. A theoretical advantage is pointed out in studying folding and unfolding processes taking place as conformational fluctuations in individual protein molecules under macroscopic equilibrium at the melting temperature. In this case, paths of folding and unfolding are shown to be identical in the statistical sense. A key to the noninteracting local structure model lies in the concept of local structures and the assumption of the absence of interactions between local structures. A local structure is defined as a continuous section of the chain which takes the same or similar local conformation as in the native conformation. The assumption of the absence of inter-actions between local structures endows the model with the remarkable character that its partition function can be calculated exactly; thereby the equilibrium population of various conformations along the folding and unfolding paths can be discussed only by a knowledge of the folded native conformation.     

Transition-state ensemble in enzyme catalysis: possibility, reality, or necessity?

Proteins are not rigid structures; they are dynamic entities, with numerous conformational isomers (substates). The dynamic nature of protein structures amplifies the structural variation of the transition state for chemical reactions performed by proteins. This suggests that utilizing a transition state ensemble to describe chemical reactions involving proteins may be a useful representation. Here we re-examine the nature of the transition state of protein chemical reactions (enzyme catalysis), considering both recent developments in chemical reaction theory (Marcus theory for SN2 reactions), and protein dynamics effects. The classical theory of chemical reactions relies on the assumption that a reaction must pass through an obligatory transition-state structure. The widely accepted view of enzymatic catalysis holds that there is tight binding of the substrate to the transition-state structure, lowering the activation energy. This picture, may, however, be oversimplified. The real meaning of a transition state is a surface, not a single saddle point on the potential energy surface. In a reaction with a "loose" transition-state structure, the entire transition-state region, rather than a single saddle point, contributes to reaction kinetics. Consequently, here we explore the validity of such a model, namely, the enzymatic modulation of the transition-state surface. We examine its utility in explaining enzyme catalysis. We analyse the possibility that instead of optimizing binding to a well-defined transition-state structure, enzymes are optimized by evolution to bind efficiently with a transition-state ensemble, with a broad range of activated conformations. For enzyme catalysis, the key issue is still transition state (ensemble) stabilization. The source of the catalytic power is the modulation of the transition state. However, our definition of the transition state is the entire transition-state surface rather just than a single well-defined structure. This view of the transition-state ensemble is consistent with the nature of the protein molecule, as embodied and depicted in the protein energy landscape of folding, and binding, funnels.     

Percolation on fitness landscapes: effects of correlation, phenotype, and incompatibilities

We study how correlations in the random fitness assignment may affect the structure of fitness landscapes, in three classes of fitness models. The first is a phenotype space in which individuals are characterized by a large number n of continuously varying traits. In a simple model of random fitness assignment, viable phenotypes are likely to form a giant connected cluster percolating throughout the phenotype space provided the viability probability is larger than 1/2(n). The second model explicitly describes genotype-to-phenotype and phenotype-to-fitness maps, allows for neutrality at both phenotype and fitness levels, and results in a fitness landscape with tunable correlation length. Here, phenotypic neutrality and correlation between fitnesses can reduce the percolation threshold, and correlations at the point of phase transition between local and global are most conducive to the formation of the giant cluster. In the third class of models, particular combinations of alleles or values of phenotypic characters are "incompatible" in the sense that the resulting genotypes or phenotypes have zero fitness. This setting can be viewed as a generalization of the canonical Bateson-Dobzhansky-Muller model of speciation and is related to K-SAT problems, prominent in computer science. We analyze the conditions for the existence of viable genotypes, their number, as well as the structure and the number of connected clusters of viable genotypes. We show that analysis based on expected values can easily lead to wrong conclusions, especially when fitness correlations are strong. We focus on pairwise incompatibilities between diallelic loci, but we also address multiple alleles, complex incompatibilities, and continuous phenotype spaces. In the case of diallelic loci, the number of clusters is stochastically bounded and each cluster contains a very large sub-cube. Finally, we demonstrate that the discrete NK model shares some signature properties of models with high correlations.     

Molecular bases of evolution

The general notions of the theory of evolution are listed. The unity of the "engineering principles" of the living nature is emphasized. The generalists and specialists species are discussed. The estimation of their evolution rates must be different if it is expressed by the number of species or by the morphological changes. The principles of "protein engineering" of the organisms and the role of metals in protein evolution are discussed. It is suggested that in the presence of ions of transition metals and zinc the Fox's proteinoids can possess more specific forms of enzymatic activity. In the evolution of language the horizontal transfer plays a much more important role than in the biological evolution. However in this case also the initial basis of the language remains. The random drift is considered and it is shown that in concordance with the neutralist theory there are no grounds to replace the calculation of the rates of mutational changes per time unity by the calculation per generation. The molecular drive is the main source of the evolutionary novelties. The drive is connected with drift. The synonymic mutations and the mutations in non-functional DNA are evolutionary important. The future mathematical theory of evolution must be based on the theory of Markov's chains with the stochastic matrix changing along the chain and containing the set of the non-diagonal members equal to zero. The results obtained in the theory of ontogeny are presented. The evolution of species is the evolution of ontogenies, the formation of the molecular theory of evolution can be possible only on the basis of the molecular theory of ontogeny. The internal causes of extinction of species reduce the accumulation of neutral and pseudo-neutral mutations.     

Solid interactions in statistical physics of biopolymers

A short survey is presented of the development of statistical physics of biological macromolecules and its modern state. The main attention is paid to the analysis of the manifestation of scale invariance and fractal properties of biopolymers--DNA and proteins. Phase transitions related to the phase structure of DNA are briefly analysed. A more detailed account is given of phase transitions in globular proteins, denaturation problem, two phases of the melted globule and the theory of heteropolymers included. Some unsolved problems of this field of science and its prospects are discussed.     

The sense of consciousness

I propose that consciousness might be understood as the property of a system that functions as a sense in the biological meaning of that term. The theory assumes that, as a complex system, the sense of consciousness is not a fixed structure but implies structure with variations and that it evolved, as many new functions do, through the integration of simpler systems. The recognized exteroceptive and enteroceptive senses provide information about the organism's environment and about the organism itself that are important to adaptation. The sense of consciousness provides information about the brain and thus about the organism and its environment. It senses other senses and processes in the brain, selecting and relating components into a form that "makes sense"-where making sense is defined as being useful to the organism in its adaptation to the environment. The theory argues that this highly adaptive organizing function evolved with the growing complexity of the brain and that it might have helped resolve discrepancies created at earlier stages. Neural energies in the brain that are the input to the sense of consciousness, along with the processing subsystem of which they are a part, constitute the base of consciousness. Consciousness itself is an emergent effect of an organizing process achieved through the sense of consciousness. The sense of consciousness thus serves an organizing function although it is not the only means of organization in the brain. Its uniqueness lies in the character of the organization it creates with consciousness as a property of that organization. The paper relates the theory to several general conceptions-interactionism, epiphenomenalism and identity theory-and illustrates a number of testable hypotheses. Viewing consciousness as a property of a sense provides a degree of conceptual integration. Much of what we know about the evolution and role of the conventionally recognized senses should help us understand the evolution and role of the sense of consciousness, and of consciousness itself.     

Transition metal binding to cod otolith proteins

Otolith microchemistry can be very useful in identifying fish populations and reconstructing fish movements. Recent attempts have been made to evaluate otoliths as proxies of ambient levels of transition metals, but findings have been inconsistent. Some of the difficulty with obtaining a definitive answer stems from an incomplete understanding of the biological control of transition metal speciation in otoliths. Metals may be incorporated as part of the calcium carbonate phase, trapped in interstitial spaces within the crystal, or associated with the protein matrix. Metal binding to the protein phase may be inferred from its structural and biochemical properties but has not been observed previously. Inherent difficulties with the extraction of metal-binding proteins in their native state from the calcium carbonate phase make them extraordinarily difficult to measure. We have developed a method that facilitates the extraction of otolith proteins without total disruption of transition metal binding. Chelating agents such as EDTA, used in the decalcification of otoliths, can demetallate the proteins if allowed to reach equilibrium; however, if the reaction is halted prior to equilibration, intact metal-protein complexes can be obtained. Using such an approach, we have confirmed the presence of copper and zinc in the soluble portion of the protein matrix of cod otoliths, and we have established that between 70% and 100% of copper and 40% to 60% of zinc found in whole otoliths are associated with the soluble part of the protein matrix. Manganese was not observed to be associated with the protein, indicating that it is either weakly bound or that no binding is present. Our results, combined with an understanding of the biological control of these metals, suggest that otoliths are not likely to be reliable indicators of copper and zinc exposure, but they may provide useful insight into fish growth and physiological development.     

The evolution of flightlessness: Is history important?

Summary Though most birds and insects are capable of flight (volant) some species are flightless. In this paper I test the hypothesis that phylogenetic constraints have played a role in the evolution of flightlessness. If speciation occurred after the evolutionary transition to flightlessness, inferences concerning the importance of particular aspects of the environment on the probability of the evolution of flightlessness may be statistically spurious because of the inflation of the sample size. Among birds, ratites and penguins illustrate the phenomenon of considerable speciation subsequent to the transition to the evolution of flightlessness. In contrast, the rails represent a group in which each flightless species probably represents a separate evolutionary transition. There are many more flightless insect species than bird species and several orders are monomorphically flightless, the sometimes enormous speciation within the order following and possibly being a consequence of the evolution of flightlessness. While it can be shown in insects that flightlessness has evolved independently many times, there are at least as many cases in which the question cannot be resolved. Therefore, in both birds and insects phylogenetic effects should not be ignored, for the number of evolutionary transitions may be much less than the number of species. The effect of incorporating phylogenetic (or at least taxonomic) constraints into the analysis of habitat factors associated with flightlessness is considered.     

无序蛋白质的判定及其结构、功能和进化特征

固有无序蛋白质(intrinsically disordered proteins,IDPs)是天然条件下自身不能折叠为明确唯一的空间结构,却具有生物学功能的一类新发现的蛋白质.这类蛋白质的发现是对传统的"结构-功能"关系认识模式的挑战.本文首先总结了无序蛋白质的实验鉴定手段、预测方法、数据库;并介绍了无序蛋白质结构(包括一级结构、二级结构、结构域无序性及变构效应)和功能特征;然后重点总结了无序蛋白质在进化角度研究的进展,包括无序区域产生的进化机制、进化速率,蛋白无序性的进化在蛋白质功能进化及生物学复杂性增加等方面的重要作用;最后展望了无序蛋白质在医药方面的应用前景.本文对于深入认识无序蛋白质的形成机制、结构和功能特征及其潜在的临床应用前景具有重要意义.